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Title: Instantaneous Normal Modes and the Protein Glass Transition

Abstract

In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at 220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes ismore » shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.« less

Authors:
 [1];  [2];  [3];  [2]
  1. University of Tennessee, Knoxville (UTK)
  2. ORNL
  3. University of Heidelberg
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
950825
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biophysical Journal; Journal Volume: 96; Journal Issue: 2
Country of Publication:
United States
Language:
English
Subject:
12 MANAGEMENT OF RADIOACTIVE WASTES, AND NON-RADIOACTIVE WASTES FROM NUCLEAR FACILITIES; EIGENVALUES; EIGENVECTORS; GLASS; HYDRATION; MINIMIZATION; NORMAL-MODE ANALYSIS; POTENTIAL ENERGY; PROTEINS; WATER

Citation Formats

Schultz, Roland, Krishnan, Marimuthu, Daidone, Isabella, and Smith, Jeremy C. Instantaneous Normal Modes and the Protein Glass Transition. United States: N. p., 2009. Web. doi:10.1016/j.bpj.2008.10.007.
Schultz, Roland, Krishnan, Marimuthu, Daidone, Isabella, & Smith, Jeremy C. Instantaneous Normal Modes and the Protein Glass Transition. United States. doi:10.1016/j.bpj.2008.10.007.
Schultz, Roland, Krishnan, Marimuthu, Daidone, Isabella, and Smith, Jeremy C. 2009. "Instantaneous Normal Modes and the Protein Glass Transition". United States. doi:10.1016/j.bpj.2008.10.007.
@article{osti_950825,
title = {Instantaneous Normal Modes and the Protein Glass Transition},
author = {Schultz, Roland and Krishnan, Marimuthu and Daidone, Isabella and Smith, Jeremy C},
abstractNote = {In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at 220 K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.},
doi = {10.1016/j.bpj.2008.10.007},
journal = {Biophysical Journal},
number = 2,
volume = 96,
place = {United States},
year = 2009,
month = 1
}
  • In the instantaneous normal mode method, normal mode analysis is performed at instantaneous configurations of a condensed-phase system, leading to modes with negative eigenvalues. These negative modes provide a means of characterizing local anharmonicities of the potential energy surface. Here, we apply instantaneous normal mode to analyze temperature-dependent diffusive dynamics in molecular dynamics simulations of a small protein (a scorpion toxin). Those characteristics of the negative modes are determined that correlate with the dynamical (or glass) transition behavior of the protein, as manifested as an increase in the gradient with T of the average atomic mean-square displacement at ~ 220more » K. The number of negative eigenvalues shows no transition with temperature. Further, although filtering the negative modes to retain only those with eigenvectors corresponding to double-well potentials does reveal a transition in the hydration water, again, no transition in the protein is seen. However, additional filtering of the protein double-well modes, so as to retain only those that, on energy minimization, escape to different regions of configurational space, finally leads to clear protein dynamical transition behavior. Partial minimization of instantaneous configurations is also found to remove nondiffusive imaginary modes. In summary, examination of the form of negative instantaneous normal modes is shown to furnish a physical picture of local diffusive dynamics accompanying the protein glass transition.« less
  • The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helpsmore » to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans and normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.« less
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